A high-performance and scalable lipase immobilization method using a dipping and jet break-up technique was reported for the production of microcapsule biocatalysts with an entrapped cascade of lipase enzyme. The lipase from Candida antarctica (CALb) recombinant Aspergillus oryzae and from the vegetal of Jatropha curcas L. (var. Sevangel) in Morelos State of Mexico were entrapped by mixing with a sodium alginate biopolymer at different concentrations. The obtained microcapsules were hardened in a CaCl2 solution, aiming at developing Ca2+ alginate microbeads with sizes mostly from 220 to 300 μm. The relationship between the process variables with the shape and size of the alginate drops before and after the gelation was established with aid of optical image analysis. The results showed that a critical Ohnesorge number (Oh) > 0.24 was required to form spherical microencapsulated beads. The biodiesel production via esterification/transesterification reaction was performed using the crude Jatropha curcas L. oil as feedstock in a batch reactor using lipase microcapsules as biocatalysts. Under the optimal reaction condition (ethanol-to-oil mass ratio: 10; water content 9.1 wt%, microencapsulated biocatalyst mass: 5.25 g, reaction temperature: 35 °C, pH of reaction mixture 7.5, stirring force 6 g), an approximately 95% fatty acid ethyl esters (FAEE) yield could be obtained. The biodiesel obtained from this work completely satisfied with the related ASTM D6751 and EN14214 standards. The microencapsulation technique reported herein allows the production of lipase microcapsules on a continuous large scale with the characteristics required for sustainable biofuel production and it can be also applied in other fields such as food processing and the pharmaceutical industry.